Hello,
The sample set summary is not generated when 100% of reads are assigned to the root and there is no line in the kraken2 report file for unclassified reads. My current workaround is to manually add
0.0 0 0 U 0 unclassified at the top of the kraken2 report, which then successfully generates the summary.
This is an example of the warning messages I get on the pavian report, in addition to the missing summary:
Hello,
The sample set summary is not generated when 100% of reads are assigned to the root and there is no line in the kraken2 report file for unclassified reads. My current workaround is to manually add
0.0 0 0 U 0 unclassifiedat the top of the kraken2 report, which then successfully generates the summary.This is an example of the warning messages I get on the pavian report, in addition to the missing summary: